- GENESIS (GENeralized-Ensemble SImulation System) is molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes. GENESIS is open source software distributed under the GPLv2 license.
- GENESIS works on typical Linux workstations, cluster machines, and massively-parallel supercomputers such as K computer at RIKEN. GPGPU calculation with CUDA enabled NVIDIA Graphics Cards is also available.
- GENESIS has been developed by the Computational Biophysics Research Team in RIKEN Center for Computational Science (R-CCS), Japan.
The GENESIS program package is composed of two MD programs (ATDYN, SPDYN) and trajectory analysis tools.
- MD, Replica Exchange MD (REMD), Energy minimization
- CPUs+GPGPUs hybrid MD/REMD simulations
- Highly parallelized PME method
- Forcefields: AMBER, CHARMM C27 & C36, Go models (Cα, all-atom, and KB Go models), etc.
- High performance MD simulations of protein solution and membrane systems by CPUs/CPUs+GPGPUs
- Scalable MD simulations of huge systems (> 100,000,000 atoms) on massively parallel environment (such as K computer)
- Multi-dimensional REMD calculations; temperature, pressure, surface tension, umbrella sampling
- String method for most probable pathway search
- Umbrella sampling, Replica Exchange Umbrella Sampling (REUS), and string method in collective variable space
- NVE, NVT, NPT, NPAT, NPγT ensembles & Langevin, Berendsen, and Bussi thermostat and barostat
- Analysis: RMSD, RMSF, PCA, WHAM, MBAR, etc.
Any published work which uses GENESIS 1.0 or before might include the reference:
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mol. Sci., 5, 310-323 (2015).
Any published work which uses GENESIS 1.1.x or 1.2.x should cite the following reference:
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita, J. Compute. Chem. 38, 2193-2206 (2017) (DOI: 10.1002/jcc.24874).
In computational neural science, there is another GENESIS (General Neuron Simulation System), which has a long history of the development. Our GENESIS has been developed independently in the computational structural biology field.